def __init__(self, biodb_selector, lineage_types_file_path="" ):
self.set_logger()
handle= biodb_selector.getFeaturesByLevel(6, 100)
i=0
for chunk in handle:
for chain in chunk:
for feature in chain:
self.feature= feature
self.lineage= Lineage(feature, biodb_selector)
lin_type= self.lineage.lineage_type
i+=1
if lin_type == 1:
continue
self.lineage_pruner= LineagePruner(self.lineage, lin_type)
log= "lineage type: %s" %lin_type
#self.logger.info(log)
if lin_type == 2:
### prune unnecessary
#print lin_type
#if len(self.lineage.taxon_list) == 6 :
# pdb.set_trace()
#print len([t.level for t in self.lineage.taxon_list])
#pass
self.lineage_pruner.prune_unnecessary()
#self.logger.info([t.level for t in self.lineage.taxon_list])
elif lin_type == 3:
### update unnecessary and prune
#pass
self.lineage_pruner.use_unnecessary_and_prune()
#pass
#self.lineage_pruner.prune_unnecessary(use=True)
elif lin_type == 4:
### TODO!: find a way to deal with!
pass
print i, self.feature.id, self.feature.name
# print i
if i % 10000 == 0:
print "########## %d taxa processed ##########" %i
class Controller(object):
def __init__(self, biodb_selector, lineage_types_file_path="" ):
self.set_logger()
handle= biodb_selector.getFeaturesByLevel(6, 100)
i=0
for chunk in handle:
for chain in chunk:
for feature in chain:
self.feature= feature
self.lineage= Lineage(feature, biodb_selector)
lin_type= self.lineage.lineage_type
i+=1
if lin_type == 1:
continue
self.lineage_pruner= LineagePruner(self.lineage, lin_type)
log= "lineage type: %s" %lin_type
#self.logger.info(log)
if lin_type == 2:
### prune unnecessary
#print lin_type
#if len(self.lineage.taxon_list) == 6 :
# pdb.set_trace()
#print len([t.level for t in self.lineage.taxon_list])
#pass
self.lineage_pruner.prune_unnecessary()
#self.logger.info([t.level for t in self.lineage.taxon_list])
elif lin_type == 3:
### update unnecessary and prune
#pass
self.lineage_pruner.use_unnecessary_and_prune()
#pass
#self.lineage_pruner.prune_unnecessary(use=True)
elif lin_type == 4:
### TODO!: find a way to deal with!
pass
print i, self.feature.id, self.feature.name
# print i
if i % 10000 == 0:
print "########## %d taxa processed ##########" %i
def set_logger(self):
# create logger with "spam application"
self.logger= logging.getLogger("dev")
self.logger.setLevel(logging.DEBUG)
# create a file handler
fh= logging.FileHandler("ncbi_taxonomy.log", mode= "w")
fh.setLevel(logging.DEBUG)
# create a console handler
#ch= logging.StreamHandler()
#ch.setLevel(logging.DEBUG)
# set formatter
#formatter = logging.Formatter("%(asctime)s - %(name)s- %(levelname)s - %(message)s",
# datefmt='%m/%d/%Y %I:%M:%S %p')
formatter = logging.Formatter("%(message)s")
fh.setFormatter(formatter)
#ch.setFormatter(formatter)
# add handlers to the logger
self.logger.addHandler(fh)
